Variant report

Variant	rs2170177
Chromosome Location	chr3:51349887-51349888
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:51348365..51351254-chr3:51421914..51424194,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145050	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10510757	0.83[CHB][hapmap];0.81[GIH][hapmap];0.89[MEX][hapmap]
rs10510758	0.80[ASN][1000 genomes]
rs12487468	0.89[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.94[LWK][hapmap];0.89[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12487496	0.84[EUR][1000 genomes]
rs12489219	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12490026	0.84[EUR][1000 genomes]
rs12490889	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12491048	0.82[ASN][1000 genomes]
rs12491836	0.84[EUR][1000 genomes]
rs12492615	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];0.91[YRI][hapmap];0.84[EUR][1000 genomes]
rs12492690	0.84[EUR][1000 genomes]
rs12493034	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12493323	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12493978	0.89[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.94[MEX][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12494979	0.80[ASN][1000 genomes]
rs12495561	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12496830	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1370124	0.81[ASN][1000 genomes]
rs1480366	1.00[ASW][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];0.83[YRI][hapmap]
rs17051685	1.00[ASW][hapmap];0.91[YRI][hapmap]
rs17051783	0.80[ASN][1000 genomes]
rs17051799	1.00[ASW][hapmap]
rs17051802	1.00[ASW][hapmap];0.88[LWK][hapmap];0.91[YRI][hapmap]
rs1809388	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1842394	0.94[CHB][hapmap];0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2061949	0.88[MEX][hapmap]
rs2086395	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2101056	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2127654	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2217938	0.80[ASN][1000 genomes]
rs2241785	0.82[ASN][1000 genomes]
rs2304512	0.80[ASN][1000 genomes]
rs2306430	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs2306431	0.89[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2355946	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2356261	0.80[ASN][1000 genomes]
rs3749317	0.80[ASN][1000 genomes]
rs3762711	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3792408	0.80[ASN][1000 genomes]
rs3804766	0.80[ASN][1000 genomes]
rs3828395	0.81[CHD][hapmap];0.89[MEX][hapmap];0.81[ASN][1000 genomes]
rs4130473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[EUR][1000 genomes]
rs4346580	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];0.83[YRI][hapmap];0.84[EUR][1000 genomes]
rs4468966	0.89[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.89[MEX][hapmap];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4687601	0.80[ASN][1000 genomes]
rs4687731	0.80[ASN][1000 genomes]
rs4687777	0.80[ASN][1000 genomes]
rs4927961	0.84[EUR][1000 genomes]
rs4974096	0.89[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.94[MEX][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4974100	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4974112	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.83[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56052360	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57047724	0.83[ASN][1000 genomes]
rs57406588	0.84[EUR][1000 genomes]
rs57603251	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs58201844	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs58836277	0.80[ASN][1000 genomes]
rs58911602	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59129045	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59682667	0.84[EUR][1000 genomes]
rs59834534	0.84[EUR][1000 genomes]
rs59953568	0.85[ASN][1000 genomes]
rs60128296	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60461297	0.84[EUR][1000 genomes]
rs60567238	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60740654	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61419317	0.80[ASN][1000 genomes]
rs61660900	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6792254	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72936442	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72936462	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72941919	0.84[EUR][1000 genomes]
rs72943166	0.84[EUR][1000 genomes]
rs72945708	0.85[ASN][1000 genomes]
rs72948197	0.84[EUR][1000 genomes]
rs72948200	0.84[EUR][1000 genomes]
rs72953143	0.84[EUR][1000 genomes]
rs72953162	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72953175	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73834252	0.80[ASN][1000 genomes]
rs73837439	0.85[ASN][1000 genomes]
rs73837442	0.80[ASN][1000 genomes]
rs73837443	0.80[ASN][1000 genomes]
rs751076	0.83[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.94[MEX][hapmap];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs880477	0.91[YRI][hapmap]
rs880478	0.89[CHB][hapmap];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9817077	1.00[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];0.89[MEX][hapmap];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9817872	1.00[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];0.89[MEX][hapmap];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9819195	0.89[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9829057	0.89[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.89[MEX][hapmap];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9856134	0.89[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.89[MEX][hapmap];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9878592	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9880909	1.00[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005858	chr3:51090373-51444027	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv536569	chr3:51090373-51444027	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	esv20206	chr3:51344873-51415825	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2170177	MAPKAPK3	cis	lymphoblastoid	seeQTL
rs2170177	HEMK	cis	multi-tissue	Pritchard

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51315400-51350000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:51340000-51370800	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr3:51341600-51372000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:51342200-51352400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr3:51342200-51353600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:51342200-51355000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:51343800-51354800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:51344200-51371800	Weak transcription	Brain Substantia Nigra	brain
9	chr3:51345000-51353400	Weak transcription	Fetal Brain Male	brain
10	chr3:51345000-51356400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr3:51345400-51354800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr3:51345600-51355400	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr3:51345600-51358000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:51347200-51350800	Strong transcription	Fetal Brain Female	brain
15	chr3:51347800-51352400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:51348000-51350000	Strong transcription	Brain Angular Gyrus	brain
17	chr3:51348000-51356400	Weak transcription	HSMMtube	muscle
18	chr3:51348200-51350000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr3:51348400-51352200	Weak transcription	Brain Germinal Matrix	brain
20	chr3:51349000-51354200	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr3:51349200-51350200	Strong transcription	Brain Inferior Temporal Lobe	brain
22	chr3:51349200-51352800	Weak transcription	Left Ventricle	heart
23	chr3:51349400-51351800	Strong transcription	Brain Anterior Caudate	brain
24	chr3:51349400-51353800	Strong transcription	Brain Cingulate Gyrus	brain
25	chr3:51349400-51358600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr3:51349600-51351800	Strong transcription	Brain Hippocampus Middle	brain

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